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Sanger sequencing of the first ~500 bp of the 16S rRNA gene is frequently used to identify bacterial pathogens that have ambiguous biochemical profiles or proteomic mass spectra. When diversity does not occur within that …
Read PDFThis study investigates the optimisation of poly(3-hydroxybutyrate) (PHB) production by Mycolicibacterium smegmatis using sugarcane bagasse (SCB) hydrolysate as a low-cost, renewable carbon source. Key fermentation parameters including temperature, pH, agitation, inoculum size and nitrogen supplementation …
Read PDFLong-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk …
Read PDFMOTIVATION: Facioscapulohumeral Muscular Dystrophy (FSHD) is an autosomal dominant form of muscular dystrophy caused by genetic or epigenetic changes within the D4Z4-repeat at the DUX4-gene, on chromosome 4q. Genetic analysis is challenging due to a …
Read PDFBACKGROUND: Direct whole genome sequencing of Capripox virus genomes from diagnostic samples is not always straightforward. Low viral content in a sample, biased sequencing and subsequent assembly and mapping methods may all influence the outcome. …
Read PDFPaenibacillus sp. TAB_01, an isolate recovered from cotton tissue culture plates and a potential novel species within the genus Paenibacillus was sequenced using Oxford Nanopore technology. The genome was 7.46 Mb with a G + …
Read PDFAdvances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality …
Read PDFZoysia macrostachya Franch. & Sav. is a halophytic perennial turfgrass in the Poaceae family, commonly found in the coastal regions of Korea, Japan, and East Asia. Z. macrostachya thrives in high-salinity environments, making it an …
Read PDFThe longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae) is a widely distributed wood-boring pest of conifers. Here, we assembled a chromosome-level genome of A. rusticus using Illumina, Oxford Nanopore, and Hi-C sequencing technologies. The assembled genome …
Read PDFBalancing replication fork progression and origin usage is essential to maintain genome stability, but measuring replication fork progression rates and origin usage throughout the genome has been challenging. Here, we use nanopore sequencing combined with …
Read PDFRNA polymerase III (Pol III) transcribes cytosolic transfer RNAs (tRNAs) and other non-coding RNAs (ncRNAs) essential to cellular function. However, many aspects of Pol III transcription and processing, including RNA modifications, remain poorly understood, mainly …
Read PDF<h4>Introduction</h4>Accessing samples from mediastinal and hilar lymph nodes is considerably more difficult, rendering the diagnosis of tuberculous mediastinal and hilar lymphadenopathy particularly challenging. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive interventional technique …
Read PDF<h4>Background</h4>The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, …
Read PDFBACKGROUND: The integration of human papillomavirus (HPV) DNA into the host genome is a key step in the development of HPV-associated cervical cancer (CC). However, the genomic characteristics of host genomic variations and HPV integration …
Read PDFThe global spread of SARS-CoV-2 was significantly impacted by the emergence of Variants of Concern (VOC), with Pakistan experiencing similar trends to other countries. To gain a comprehensive understanding of the genomic epidemiology of SARS-CoV-2 …
Read PDF2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2'-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for …
Read PDFWe report complete circular genomes of five <i>Janthinobacterium lividum</i> strains isolated from Austrian freshwater sources. Genomes (6.3-6.6 Mbp, >99% complete) were assembled using Oxford Nanopore sequencing. Each encodes a full violacein biosynthesis pathway. Phylogenomic analysis …
Read PDFAlaska has the highest incidence of tuberculosis (TB) in the United States, with 8% mortality while undergoing TB treatment. With a quarter of TB cases lacking sputum culture to enable drug resistance testing, FreezeTB aimed …
Read PDFFermented shrimp paste (Kapi) is a culturally significant condiment valued for its flavor and nutritional value. However, inconsistent production practices may lead to microbial contamination and histamine accumulation, posing health risks. Understanding microbial diversity, salt-tolerant …
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